Cloud and Tifa still aren't living together in Dirge of Cerberus (the chronologically furthest along game in the entire FFVII universe), Tifa's not pregnant with Cloud Jr., and FFS, she rides with Barret (read: NOT CLOUD) into the big battle with Deepground near the end. And to my knowledge, they don't even interact at all in that game.
The "Tifa isn't pregnant" and "she doesn't ride into the big battle with Cloud" as evidence that her and Cloud aren't together are just too stupid.
So what if Tifa isn't pregnant? I mean, really? You're using that as evidence that they aren't together?! Well, Aerith wasn't pregnant when she died, so that must mean that Cloud and her aren't together!
Also, Tifa not going into battle with Cloud means nothing. Their positions in the battle were probably chosen by some general or leader in WRO, and they probably had no influence or say on where they would be. Saying that, because Tifa didn't ride with Cloud into battle, makes as much sense as saying that her and Barret are together because she was with him.
But... when is it stated in DoC that Cloud and Tifa aren't living together? I haven't played the game in forever (and I haven't played it very much, at that) so I can't remember if that was stated or not. Or, did Nomura say that they weren't in an interview or something?
Also, they totally interact in the game. Not a whole lot because DoC is focused on Vincent, but they do interact.